ERROR NetCDF: Invalid dimension size

Run-time issues concerning Yambo that are not covered in the above forums.

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burkzdemir
Posts: 61
Joined: Tue Sep 09, 2014 7:57 pm

ERROR NetCDF: Invalid dimension size

Post by burkzdemir » Wed Jan 29, 2020 11:45 am

Dear Yambo developers,

I am trying to run GW+BSE calculation for a layered material but I am getting this error. What could be the reason?

|Random points [col]:0
- S/N 004105 -------------------------- v.04.04.00 r.00148 -

[05.04.03] Kernel loop
======================


[ERROR] STOP signal received while in :[05.04.03] Kernel loop

[ERROR] File ./SAVE//ndb.BS_Q1_CPU_0; Variable W_DbGd; NetCDF: Invalid dimension size
Burak Ozdemir
Post-doc,
University of Ostrava, Ostrava, Czech Republic

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Daniele Varsano
Posts: 2723
Joined: Tue Mar 17, 2009 2:23 pm
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Re: ERROR NetCDF: Invalid dimension size

Post by Daniele Varsano » Wed Jan 29, 2020 11:07 pm

Dear Burak,
in order to spot the problem, can you post your input/report and eventually log files?
Best,
Daniele
Dr. Daniele Varsano
S3-CNR Institute of Nanoscience and MaX Center, Italy
MaX - Materials design at the Exascale
http://www.nano.cnr.it
http://www.max-centre.eu/

burkzdemir
Posts: 61
Joined: Tue Sep 09, 2014 7:57 pm

Re: ERROR NetCDF: Invalid dimension size

Post by burkzdemir » Wed Jan 29, 2020 11:28 pm

Dear Daniele,

Here is a link to dropbox file

https://www.dropbox.com/sh/gu2i4eli8zhh ... MRV1a?dl=0

Best regards,
Burak Ozdemir
Post-doc,
University of Ostrava, Ostrava, Czech Republic

User avatar
Daniele Varsano
Posts: 2723
Joined: Tue Mar 17, 2009 2:23 pm
Contact:

Re: ERROR NetCDF: Invalid dimension size

Post by Daniele Varsano » Wed Jan 29, 2020 11:56 pm

Dear Burak,
actually, from your report file I can see there is a lot of confusion, many databases are read from previous runs which are not compatible with the actual input (check ERR and WRN in your report file).
I suggest you to start the calculation from scratch in a clean directory.
Some advise:

BSENGBlk=1 and NGsBlkXp=1 it is for sure not converged, you are totally neglecting the nonlocality of the screening, these are parameters that need to be converged.

Code: Select all

% BndsRnXp
   15 |  25 |                   # [Xp] Polarization function bands
%
Summation bands in the response function, this is a sum-over-state, it is really dangerous to neglect valence bands, it is recommendable to include all the valence bands and increase the conduction bands.

Code: Select all

% BSEBands
   1 |  40 |                   # [BSK] Bands range
%
Most surely you do not need to include such a big number of bands, in particular, deep valence bands, few bands around the Fermi energy are usually enough to converge a BSE spectrum. I would start from a 19-23 windows and increase it little by little. Surely I would not include the first bands, this will make the BSE matrix very large without reason.

Best,
Daniele
Dr. Daniele Varsano
S3-CNR Institute of Nanoscience and MaX Center, Italy
MaX - Materials design at the Exascale
http://www.nano.cnr.it
http://www.max-centre.eu/

burkzdemir
Posts: 61
Joined: Tue Sep 09, 2014 7:57 pm

Re: ERROR NetCDF: Invalid dimension size

Post by burkzdemir » Tue Oct 20, 2020 12:00 pm

Dear Daniele,

Thank you for your suggestions. I fixed it. But, now I got the same error but I believe this time for another reason. Can you please look at my files.

Code: Select all

#                                                           
# :::   :::   :::     ::::    ::::  :::::::::   ::::::::    
# :+:   :+: :+: :+:   +:+:+: :+:+:+ :+:    :+: :+:    :+:   
#  +:+ +:+ +:+   +:+  +:+ +:+:+ +:+ +:+    +:+ +:+    +:+   
#   +#++: +#++:++#++: +#+  +:+  +#+ +#++:++#+  +#+    +:+   
#    +#+  +#+     +#+ +#+       +#+ +#+    +#+ +#+    +#+   
#    #+#  #+#     #+# #+#       #+# #+#    #+# #+#    #+#   
#    ###  ###     ### ###       ### #########   ########    
#                                                           
#                                                           
# GPL Version 4.4.0 Revision 148. (Based on r.16920 h.961a8d
#                        MPI Build                          
#                http://www.yambo-code.org                  
#
optics                         # [R OPT] Optics
bss                            # [R BSS] Bethe Salpeter Equation solver
bse                            # [R BSE] Bethe Salpeter Equation.
bsk                            # [R BSK] Bethe Salpeter Equation kernel
em1d                           # [R Xd] Dynamical Inverse Dielectric Matrix
ppa                            # [R Xp] Plasmon Pole Approximation
Chimod= "HARTREE"              # [X] IP/Hartree/ALDA/LRC/PF/BSfxc
BSEmod= "retarded"             # [BSE] resonant/retarded/coupling
BSKmod= "SEX"                  # [BSE] IP/Hartree/HF/ALDA/SEX
BSSmod= "h"                    # [BSS] (h)aydock/(d)iagonalization/(i)nversion/(t)ddft`
BSENGexx=  50541       RL      # [BSK] Exchange components
BSENGBlk= 27           RL      # [BSK] Screened interaction block size
#WehCpl                        # [BSK] eh interaction included also in coupling
KfnQPdb= "E < ./SAVE/ndb.QP"                # [EXTQP BSK BSS] Database
KfnQP_N= 1                     # [EXTQP BSK BSS] Interpolation neighbours
% KfnQP_E
 0.000000 | 1.000000 | 1.000000 |        # [EXTQP BSK BSS] E parameters  (c/v) eV|adim|adim
%
KfnQP_Z= ( 1.000000 , 0.000000 )       # [EXTQP BSK BSS] Z factor  (c/v)
KfnQP_Wv_E= 0.000000   eV      # [EXTQP BSK BSS] W Energy reference  (valence)
% KfnQP_Wv
 0.00     | 0.00     | 0.00     |        # [EXTQP BSK BSS] W parameters  (valence) eV| 1|eV^-1
%
KfnQP_Wv_dos= 0.000000 eV      # [EXTQP BSK BSS] W dos pre-factor  (valence)
KfnQP_Wc_E= 0.000000   eV      # [EXTQP BSK BSS] W Energy reference  (conduction)
% KfnQP_Wc
 0.00     | 0.00     | 0.00     |        # [EXTQP BSK BSS] W parameters  (conduction) eV| 1 |eV^-1
%
KfnQP_Wc_dos= 0.000000 eV      # [EXTQP BSK BSS] W dos pre-factor  (conduction)
% BEnRange
  0.300000 | 5.00000 | eV      # [BSS] Energy range
%
% BDmRange
  0.010000 |  0.010000 | eV      # [BSS] Damping range
%
BEnSteps= 100                  # [BSS] Energy steps
% BLongDir
 1.000000 | 0.000000 | 0.000000 |        # [BSS] [cc] Electric Field
%
% BSEBands
   6 | 26 |                   # [BSK] Bands range
%
BSHayTrs= -0.002000             # [BSS] Relative [o/o] Haydock threshold. Strict(>0)/Average(<0)
XfnQPdb= "none"                # [EXTQP Xd] Database
XfnQP_N= 1                     # [EXTQP Xd] Interpolation neighbours
% XfnQP_E
 0.000000 | 1.000000 | 1.000000 |        # [EXTQP Xd] E parameters  (c/v) eV|adim|adim
%
XfnQP_Z= ( 1.000000 , 0.000000 )       # [EXTQP Xd] Z factor  (c/v)
XfnQP_Wv_E= 0.000000   eV      # [EXTQP Xd] W Energy reference  (valence)
% XfnQP_Wv
 0.00     | 0.00     | 0.00     |        # [EXTQP Xd] W parameters  (valence) eV| 1|eV^-1
%
XfnQP_Wv_dos= 0.000000 eV      # [EXTQP Xd] W dos pre-factor  (valence)
XfnQP_Wc_E= 0.000000   eV      # [EXTQP Xd] W Energy reference  (conduction)
% XfnQP_Wc
 0.00     | 0.00     | 0.00     |        # [EXTQP Xd] W parameters  (conduction) eV| 1 |eV^-1
%
XfnQP_Wc_dos= 0.000000 eV      # [EXTQP Xd] W dos pre-factor  (conduction)
% BndsRnXp
   1 | 200 |                   # [Xp] Polarization function bands
%
NGsBlkXp= 27           RL      # [Xp] Response block size
% LongDrXp
 1.000000 | 0.000000 | 0.000000 |        # [Xp] [cc] Electric Field
%
PPAPntXp= 27.21138     eV      # [Xp] PPA imaginary energy
This is the link to gdrive file containing the report files. https://drive.google.com/drive/folders/ ... sp=sharing

Thank you,
Burak Ozdemir
Post-doc,
University of Ostrava, Ostrava, Czech Republic

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Daniele Varsano
Posts: 2723
Joined: Tue Mar 17, 2009 2:23 pm
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Re: ERROR NetCDF: Invalid dimension size

Post by Daniele Varsano » Wed Oct 21, 2020 8:20 am

Dear Burak,
it is not easy to understand what is happening here? It seems you have a problem with the double grid, but you are not using it.
In order to look things deeper can you post the following information:
1) In your SAVE directory:
> ncdump ndb.BS_Q1_CPU_0 > ndb.BS_Q1_CPU_0.txt
and from the .txt file report all the lines where W_DbGd appears

2) post your nscf QE file, it is possible there is some problem in the k point definition.

Best,
Daniele
Dr. Daniele Varsano
S3-CNR Institute of Nanoscience and MaX Center, Italy
MaX - Materials design at the Exascale
http://www.nano.cnr.it
http://www.max-centre.eu/

burkzdemir
Posts: 61
Joined: Tue Sep 09, 2014 7:57 pm

Re: ERROR NetCDF: Invalid dimension size

Post by burkzdemir » Thu Oct 22, 2020 6:56 pm

Dear Daniele,

Here is the information you would like to see.

float W_DbGd(D_0000000002) ;

W_DbGd = 0, 0 ;

Code: Select all

 &control
    calculation = 'nscf',
    restart_mode='from_scratch',
    prefix='Si',
    pseudo_dir = './',
    outdir='./tmp',
    wf_collect=.true.
 /
&SYSTEM
  ibrav = 0, A = 5.43, nat = 8, ntyp = 1,
  ecutwfc=50,
  nbnd=200
  force_symmorphic=.true.
/
 &electrons
    mixing_beta = 0.7,
 /
 &ions
 /
 &cell
 /
ATOMIC_SPECIES
   Si   12.01060  Si.pz-n-nc.UPF
ATOMIC_POSITIONS {alat}
Si       0.000000000   0.000000000   0.000000000
Si       0.496087301   0.496087301   0.000000000
Si       0.496087301   0.000000000   0.496087301
Si       0.000000000   0.496087301   0.496087301
Si       0.248044632   0.248044632   0.248044632
Si       0.744129971   0.248044632   0.744129971
Si       0.744129971   0.744129971   0.248044632
Si       0.248044632   0.744129971   0.744129971
CELL_PARAMETERS {alat}
   0.992174603   0.000000000   0.000000000
   0.000000000   0.992174603   0.000000000
   0.000000000   0.000000000   0.992174603
K_POINTS {automatic}
16 16 16 0 0 0
Thank you,
Burak Ozdemir
Post-doc,
University of Ostrava, Ostrava, Czech Republic

User avatar
Daniele Varsano
Posts: 2723
Joined: Tue Mar 17, 2009 2:23 pm
Contact:

Re: ERROR NetCDF: Invalid dimension size

Post by Daniele Varsano » Fri Oct 23, 2020 6:17 am

Dear Burak,
I can't see anything wrong in your input file.
I just noticed you are using a 4.4 release of Yambo, I strongly suggest you update to the latest version (4.5) and repeat your calculations.
If the problem persists we should reproduce your error. In the latter case, I will ask you to prepare input files for a quick calculation where the problem appears.

Best,
Daniele
Dr. Daniele Varsano
S3-CNR Institute of Nanoscience and MaX Center, Italy
MaX - Materials design at the Exascale
http://www.nano.cnr.it
http://www.max-centre.eu/

burkzdemir
Posts: 61
Joined: Tue Sep 09, 2014 7:57 pm

Re: ERROR NetCDF: Invalid dimension size

Post by burkzdemir » Sun Oct 25, 2020 8:44 pm

Dear Daniele,

I installed the latest version of Yambo and obtained the same error. You can find my input files in the link below.

https://drive.google.com/file/d/12-HcJs ... sp=sharing

Best,
Burak Ozdemir
Post-doc,
University of Ostrava, Ostrava, Czech Republic

User avatar
Daniele Varsano
Posts: 2723
Joined: Tue Mar 17, 2009 2:23 pm
Contact:

Re: ERROR NetCDF: Invalid dimension size

Post by Daniele Varsano » Mon Oct 26, 2020 7:32 am

Dear Burak,
can you post also the report and log files, moreover can you repeat your calculation with a more clean input file?
In the BSE you are using both static (em1s) and dynamic (ppa) screening and relative variables, moreover they are not compatible (different number of G vectors). This is not needed, just choose one of them. If we will need to reproduce your error it is practical to have a fast calculation presenting the problem, can you prepare a quick example showing the error (e.g. you are using a very large number of BSE bands that most probably are not needed).

Best,
Daniele
Dr. Daniele Varsano
S3-CNR Institute of Nanoscience and MaX Center, Italy
MaX - Materials design at the Exascale
http://www.nano.cnr.it
http://www.max-centre.eu/

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